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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi Ralf,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">The t_den and r_den additions made the difference (also needed with the change_of_basis_op using rt_mx as starting point) – may be worth adding as an additional
comment in the __init__ methods what these actually mean as it was not clear!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Many thanks,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Graeme<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> cctbxbb-bounces@phenix-online.org [mailto:cctbxbb-bounces@phenix-online.org]
<b>On Behalf Of </b>Ralf Grosse-Kunstleve<br>
<b>Sent:</b> 12 July 2011 20:18<br>
<b>To:</b> cctbx mailing list<br>
<b>Subject:</b> Re: [cctbxbb] Conversion from symmetry operation to matrix<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Graeme,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">You can make it work like this:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New"">def symop_to_mat(symop):</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New""> return matrix.sqr(sgtbx.rt_mx(</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New""> sgtbx.parse_string(symop)<span style="color:red">, r_den=12, t_den=144</span>).as_double_array()[:9]).transpose().elems</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">But I suggest using the change_of_basis_op type instead. See the complete script below.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Ralf<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New"">from cctbx import sgtbx</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New"">from cctbx.array_family import flex</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New"">from scitbx import matrix</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New"">def symop_to_mat(symop):</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New""> return matrix.sqr(sgtbx.rt_mx(</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New""> sgtbx.parse_string(symop), r_den=12, t_den=144).as_double_array()[:9]).transpose().elems</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New"">def run(args):</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New""> assert len(args) == 0</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New""> print symop_to_mat("1/2*z,-y+1/2*z,x")</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New""> cb_op = sgtbx.change_of_basis_op("1/2*z,-y+1/2*z,x").inverse()</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New""> print cb_op.as_hkl()</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New""> miller_indices = flex.miller_index([(2,4,1)])</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New""> print list(cb_op.apply(miller_indices))</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New"">if (__name__ == "__main__"):</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New""> import sys</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New""> run(args=sys.argv[1:])</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Tue, Jul 12, 2011 at 7:06 AM, <<a href="mailto:Graeme.Winter@diamond.ac.uk">Graeme.Winter@diamond.ac.uk</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Dear All,<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">For a little while now I have been using some cctbx jiffy code to convert from symmetry operations to matrices to help with testing reindexing data. This works as<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">def symop_to_mat(symop):<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> return matrix.sqr(sgtbx.rt_mx(<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> sgtbx.parse_string(symop)).as_double_array()[:9]).transpose().elems<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Which is plenty simple. However it just exploded when given “1/2*z,-y+1/2*z,x” - reasonably really as this is not a rotation. It is however a valid reindexing operation to go from
C2 to P1.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Does anyone have code which will handle this general transformation from a reindexing operation to a matrix, which will cope with the fact that the resulting matrix is not RT? I
had a little jiffy I wrote using ccp4f lib (symop2mat – you can probably see it!) but I am trying to do away with things like that and do everything properly…<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Many thanks in advance,<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Graeme<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Dr. Graeme Winter<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Senior Software Scientist<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Diamond Light Source<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><a href="tel:%2B44%201235%20778091" target="_blank">+44 1235 778091</a> (work)<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><a href="tel:%2B44%207786%20662784" target="_blank">+44 7786 662784</a> (work mobile)<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p> <o:p></o:p></p>
<p>-- <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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